From the Designs FAQ on Magna-Hoop Software:
Q: I am using Magna-Hoop Software to save my properly sized designs and load them into my machine. Why doesn’t it center the design in the opening like it does on the screen?
A: Magna-Hoop Software is a sizing program that allows you to load designs and fit them to the openings in Magna-Hoop and Quick-Snap. One advantage of the software is that you know they are sized properly to fit the opening.
However, when the design is loaded into the embroidery machine, the machine has no way of identifying which hoop or opening you have selected; only that there is a design and a hoop. It will always default to the machine center, which is not necessarily the hoop or the opening center. In other words, different machines have different methods of deciding what hoop is on the machine, if it decides at all.
It is the user's responsibility to tell the machine where to stitch the design. You must relocate the design, which has been correctly sized, to the center of the opening where it is to be stitched. With some machines (including the Janome MB4) this may also involve overriding the hoop designation assigned by the machine based on the design size.
ALWAYS trace the design to make sure the needle will clear the frame.
Note- the software has a print feature which allows for the printing of placement templates. Select the option to print the Magna-Frame and an outline of the frame will print with the design. Use it to help locate your needle to the center of the design.
I hope this helps to clarify the software's capabilities.